Starting phenix.real_space_refine on Thu Nov 14 20:53:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi9_40063/11_2024/8gi9_40063.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi9_40063/11_2024/8gi9_40063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi9_40063/11_2024/8gi9_40063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi9_40063/11_2024/8gi9_40063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi9_40063/11_2024/8gi9_40063.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi9_40063/11_2024/8gi9_40063.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.222 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 39 5.16 5 Na 9 4.78 5 C 4842 2.51 5 N 894 2.21 5 O 1062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6852 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1948 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain: "A" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 336 Unusual residues: {' NA': 3, 'CLR': 7, 'PEE': 2, 'RET': 1} Classifications: {'undetermined': 13, 'water': 15} Link IDs: {None: 27} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Restraints were copied for chains: C, B Time building chain proxies: 4.41, per 1000 atoms: 0.64 Number of scatterers: 6852 At special positions: 0 Unit cell: (79.31, 78.28, 76.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 6 15.00 Na 9 11.00 O 1062 8.00 N 894 7.00 C 4842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 821.0 milliseconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1326 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 79.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 removed outlier: 3.562A pdb=" N ASP A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 removed outlier: 3.523A pdb=" N ASN A 67 " --> pdb=" O PRO A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.570A pdb=" N CYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.576A pdb=" N VAL A 107 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 109 through 122 Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 150 through 177 Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.904A pdb=" N LEU A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.755A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 48 removed outlier: 3.562A pdb=" N ASP B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 67 removed outlier: 3.523A pdb=" N ASN B 67 " --> pdb=" O PRO B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 68 through 90 removed outlier: 3.570A pdb=" N CYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.576A pdb=" N VAL B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 109 through 122 Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 150 through 177 Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 181 through 199 removed outlier: 3.904A pdb=" N LEU B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.755A pdb=" N ILE B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 48 removed outlier: 3.562A pdb=" N ASP C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 67 removed outlier: 3.522A pdb=" N ASN C 67 " --> pdb=" O PRO C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 68 through 90 removed outlier: 3.570A pdb=" N CYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.576A pdb=" N VAL C 107 " --> pdb=" O TYR C 103 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 150 through 177 Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 181 through 199 removed outlier: 3.904A pdb=" N LEU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.755A pdb=" N ILE C 204 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 408 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1518 1.33 - 1.45: 1521 1.45 - 1.57: 3876 1.57 - 1.69: 114 1.69 - 1.81: 57 Bond restraints: 7086 Sorted by residual: bond pdb=" O4P PEE A 312 " pdb=" P PEE A 312 " ideal model delta sigma weight residual 1.653 1.786 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" O4P PEE B 312 " pdb=" P PEE B 312 " ideal model delta sigma weight residual 1.653 1.786 -0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" O4P PEE C 312 " pdb=" P PEE C 312 " ideal model delta sigma weight residual 1.653 1.785 -0.132 2.00e-02 2.50e+03 4.39e+01 bond pdb=" O4P PEE B 313 " pdb=" P PEE B 313 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" O4P PEE A 313 " pdb=" P PEE A 313 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 9300 2.72 - 5.44: 318 5.44 - 8.15: 78 8.15 - 10.87: 3 10.87 - 13.59: 6 Bond angle restraints: 9705 Sorted by residual: angle pdb=" O1P PEE B 312 " pdb=" P PEE B 312 " pdb=" O2P PEE B 312 " ideal model delta sigma weight residual 119.43 133.02 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE A 312 " pdb=" P PEE A 312 " pdb=" O2P PEE A 312 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE C 312 " pdb=" P PEE C 312 " pdb=" O2P PEE C 312 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE B 313 " pdb=" P PEE B 313 " pdb=" O2P PEE B 313 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE A 313 " pdb=" P PEE A 313 " pdb=" O2P PEE A 313 " ideal model delta sigma weight residual 119.43 133.00 -13.57 3.00e+00 1.11e-01 2.05e+01 ... (remaining 9700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 4794 29.20 - 58.39: 168 58.39 - 87.59: 21 87.59 - 116.78: 12 116.78 - 145.98: 9 Dihedral angle restraints: 5004 sinusoidal: 2922 harmonic: 2082 Sorted by residual: dihedral pdb=" C32 PEE A 312 " pdb=" C30 PEE A 312 " pdb=" C31 PEE A 312 " pdb=" O3 PEE A 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.86 -145.98 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C32 PEE C 312 " pdb=" C30 PEE C 312 " pdb=" C31 PEE C 312 " pdb=" O3 PEE C 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.87 -145.97 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C32 PEE B 312 " pdb=" C30 PEE B 312 " pdb=" C31 PEE B 312 " pdb=" O3 PEE B 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.89 -145.95 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 5001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 892 0.078 - 0.157: 74 0.157 - 0.235: 3 0.235 - 0.313: 54 0.313 - 0.391: 33 Chirality restraints: 1056 Sorted by residual: chirality pdb=" C2 PEE A 312 " pdb=" C1 PEE A 312 " pdb=" C3 PEE A 312 " pdb=" O2 PEE A 312 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C2 PEE C 312 " pdb=" C1 PEE C 312 " pdb=" C3 PEE C 312 " pdb=" O2 PEE C 312 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C17 CLR A 305 " pdb=" C13 CLR A 305 " pdb=" C16 CLR A 305 " pdb=" C20 CLR A 305 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 1053 not shown) Planarity restraints: 1035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 94 " 0.015 5.00e-02 4.00e+02 2.27e-02 8.24e-01 pdb=" N PRO A 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 94 " 0.015 5.00e-02 4.00e+02 2.26e-02 8.18e-01 pdb=" N PRO C 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 94 " 0.015 5.00e-02 4.00e+02 2.25e-02 8.12e-01 pdb=" N PRO B 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.013 5.00e-02 4.00e+02 ... (remaining 1032 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 39 2.48 - 3.09: 4814 3.09 - 3.69: 9987 3.69 - 4.30: 16770 4.30 - 4.90: 27808 Nonbonded interactions: 59418 Sorted by model distance: nonbonded pdb=" OH TYR B 62 " pdb=" OE1 GLN C 175 " model vdw 1.878 3.040 nonbonded pdb=" OH TYR A 62 " pdb=" OE1 GLN B 175 " model vdw 1.878 3.040 nonbonded pdb=" OE1 GLN A 175 " pdb=" OH TYR C 62 " model vdw 1.878 3.040 nonbonded pdb=" O ALA A 132 " pdb=" OG1 THR A 136 " model vdw 2.243 3.040 nonbonded pdb=" O ALA B 132 " pdb=" OG1 THR B 136 " model vdw 2.243 3.040 ... (remaining 59413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 18.330 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.133 7086 Z= 0.572 Angle : 1.113 13.589 9705 Z= 0.394 Chirality : 0.100 0.391 1056 Planarity : 0.003 0.023 1035 Dihedral : 15.912 145.981 3678 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.33), residues: 714 helix: 1.73 (0.24), residues: 504 sheet: None (None), residues: 0 loop : -1.58 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 190 HIS 0.002 0.001 HIS A 225 PHE 0.005 0.001 PHE B 221 TYR 0.006 0.001 TYR C 177 ARG 0.001 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8221 (t0) cc_final: 0.7866 (t0) REVERT: A 186 LYS cc_start: 0.7719 (mptt) cc_final: 0.7415 (ttmm) REVERT: B 144 PHE cc_start: 0.7667 (t80) cc_final: 0.7043 (t80) REVERT: B 186 LYS cc_start: 0.7894 (mptt) cc_final: 0.7558 (ttmm) REVERT: C 186 LYS cc_start: 0.7595 (mptt) cc_final: 0.7142 (ttmm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 1.2732 time to fit residues: 101.9984 Evaluate side-chains 68 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.0470 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 7086 Z= 0.372 Angle : 1.040 17.106 9705 Z= 0.514 Chirality : 0.057 0.513 1056 Planarity : 0.015 0.304 1035 Dihedral : 16.551 161.434 2445 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.48 % Favored : 95.38 % Rotamer: Outliers : 1.63 % Allowed : 4.58 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.30), residues: 714 helix: 0.45 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -2.37 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.010 TRP B 210 HIS 0.031 0.003 HIS C 125 PHE 0.156 0.005 PHE C 144 TYR 0.088 0.006 TYR B 81 ARG 0.122 0.006 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.648 Fit side-chains REVERT: A 116 ASP cc_start: 0.8169 (t0) cc_final: 0.7900 (t0) REVERT: A 174 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7106 (mtmm) REVERT: A 186 LYS cc_start: 0.7558 (mptt) cc_final: 0.7262 (ttmm) REVERT: B 144 PHE cc_start: 0.7500 (t80) cc_final: 0.6875 (t80) REVERT: B 186 LYS cc_start: 0.7787 (mptt) cc_final: 0.7422 (ttmm) REVERT: B 240 MET cc_start: 0.8477 (tpt) cc_final: 0.8264 (mmm) REVERT: C 186 LYS cc_start: 0.7504 (mptt) cc_final: 0.7067 (ttmm) REVERT: C 240 MET cc_start: 0.8577 (mmp) cc_final: 0.8346 (tpt) outliers start: 10 outliers final: 1 residues processed: 72 average time/residue: 1.2624 time to fit residues: 96.0901 Evaluate side-chains 69 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain B residue 109 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7086 Z= 0.247 Angle : 0.588 6.153 9705 Z= 0.275 Chirality : 0.041 0.252 1056 Planarity : 0.006 0.062 1035 Dihedral : 15.126 179.067 2445 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.31 % Allowed : 5.56 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.31), residues: 714 helix: 1.64 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.16 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 161 HIS 0.006 0.001 HIS C 125 PHE 0.018 0.001 PHE A 144 TYR 0.015 0.002 TYR C 154 ARG 0.004 0.001 ARG C 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.667 Fit side-chains REVERT: A 116 ASP cc_start: 0.8358 (t0) cc_final: 0.8153 (t0) REVERT: A 183 LYS cc_start: 0.8003 (ttpp) cc_final: 0.7782 (ttpp) REVERT: A 186 LYS cc_start: 0.7639 (mptt) cc_final: 0.7395 (ttmm) REVERT: B 144 PHE cc_start: 0.7604 (t80) cc_final: 0.7121 (m-80) REVERT: B 186 LYS cc_start: 0.7806 (mptt) cc_final: 0.7489 (ttmm) REVERT: C 183 LYS cc_start: 0.8194 (tppp) cc_final: 0.7918 (ttmt) REVERT: C 186 LYS cc_start: 0.7666 (mptt) cc_final: 0.7270 (ttmm) outliers start: 8 outliers final: 1 residues processed: 77 average time/residue: 1.2996 time to fit residues: 105.6700 Evaluate side-chains 66 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7086 Z= 0.189 Angle : 0.524 5.943 9705 Z= 0.244 Chirality : 0.039 0.223 1056 Planarity : 0.005 0.052 1035 Dihedral : 14.237 162.949 2445 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.82 % Allowed : 8.82 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.31), residues: 714 helix: 2.03 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.10 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 161 HIS 0.004 0.001 HIS C 125 PHE 0.017 0.001 PHE A 144 TYR 0.011 0.001 TYR B 154 ARG 0.004 0.001 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.670 Fit side-chains REVERT: A 106 TYR cc_start: 0.8726 (m-10) cc_final: 0.8439 (m-80) REVERT: A 171 ARG cc_start: 0.7388 (ttp-110) cc_final: 0.7146 (ttp-110) REVERT: A 186 LYS cc_start: 0.7605 (mptt) cc_final: 0.7379 (ttmm) REVERT: B 65 GLU cc_start: 0.6812 (tp30) cc_final: 0.6513 (tp30) REVERT: B 186 LYS cc_start: 0.7821 (mptt) cc_final: 0.7542 (ttmm) REVERT: C 175 GLN cc_start: 0.7270 (tt0) cc_final: 0.6595 (mp10) REVERT: C 186 LYS cc_start: 0.7693 (mptt) cc_final: 0.7319 (ttmm) outliers start: 5 outliers final: 2 residues processed: 84 average time/residue: 1.2297 time to fit residues: 109.2070 Evaluate side-chains 76 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7086 Z= 0.218 Angle : 0.536 5.790 9705 Z= 0.249 Chirality : 0.039 0.206 1056 Planarity : 0.005 0.055 1035 Dihedral : 13.865 144.256 2445 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.47 % Allowed : 10.46 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.31), residues: 714 helix: 2.09 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.09 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 161 HIS 0.003 0.001 HIS C 125 PHE 0.016 0.001 PHE A 144 TYR 0.014 0.001 TYR B 177 ARG 0.003 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 106 TYR cc_start: 0.8728 (m-10) cc_final: 0.8469 (m-80) REVERT: A 171 ARG cc_start: 0.7441 (ttp-110) cc_final: 0.7201 (ttp-110) REVERT: A 176 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6813 (tpt90) REVERT: A 186 LYS cc_start: 0.7678 (mptt) cc_final: 0.7371 (ttmm) REVERT: B 65 GLU cc_start: 0.6735 (tp30) cc_final: 0.6476 (tp30) REVERT: B 144 PHE cc_start: 0.7561 (t80) cc_final: 0.7231 (t80) REVERT: B 186 LYS cc_start: 0.7829 (mptt) cc_final: 0.7519 (ttmm) REVERT: C 175 GLN cc_start: 0.7416 (tt0) cc_final: 0.6649 (mp10) REVERT: C 186 LYS cc_start: 0.7695 (mptt) cc_final: 0.7379 (ttmm) outliers start: 9 outliers final: 3 residues processed: 84 average time/residue: 1.2930 time to fit residues: 114.5427 Evaluate side-chains 81 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.0170 chunk 17 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7086 Z= 0.186 Angle : 0.514 5.602 9705 Z= 0.239 Chirality : 0.038 0.191 1056 Planarity : 0.005 0.055 1035 Dihedral : 13.444 134.169 2445 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.80 % Allowed : 10.62 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.31), residues: 714 helix: 2.20 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.06 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.003 0.001 HIS C 125 PHE 0.019 0.001 PHE A 144 TYR 0.010 0.001 TYR B 177 ARG 0.002 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 106 TYR cc_start: 0.8727 (m-10) cc_final: 0.8426 (m-80) REVERT: A 176 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6830 (tpt90) REVERT: A 186 LYS cc_start: 0.7691 (mptt) cc_final: 0.7400 (ttmm) REVERT: B 21 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.7014 (t70) REVERT: B 24 LEU cc_start: 0.7944 (tp) cc_final: 0.7742 (tp) REVERT: B 144 PHE cc_start: 0.7641 (t80) cc_final: 0.7297 (t80) REVERT: B 186 LYS cc_start: 0.7807 (mptt) cc_final: 0.7488 (ttmm) REVERT: C 170 LEU cc_start: 0.8315 (tp) cc_final: 0.8014 (tp) REVERT: C 175 GLN cc_start: 0.7334 (tt0) cc_final: 0.6624 (mp10) REVERT: C 186 LYS cc_start: 0.7675 (mptt) cc_final: 0.7357 (ttmm) outliers start: 11 outliers final: 3 residues processed: 84 average time/residue: 1.3230 time to fit residues: 117.0935 Evaluate side-chains 81 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 0.0060 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS C 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7086 Z= 0.181 Angle : 0.510 5.615 9705 Z= 0.236 Chirality : 0.038 0.182 1056 Planarity : 0.005 0.046 1035 Dihedral : 13.093 128.010 2445 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.14 % Allowed : 11.60 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.31), residues: 714 helix: 2.24 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.02 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.002 0.001 HIS C 125 PHE 0.017 0.001 PHE A 144 TYR 0.010 0.001 TYR B 177 ARG 0.002 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6889 (ttt90) REVERT: A 186 LYS cc_start: 0.7695 (mptt) cc_final: 0.7395 (ttmm) REVERT: B 21 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6677 (t0) REVERT: B 144 PHE cc_start: 0.7627 (t80) cc_final: 0.7288 (t80) REVERT: B 186 LYS cc_start: 0.7793 (mptt) cc_final: 0.7487 (ttmm) REVERT: C 170 LEU cc_start: 0.8290 (tp) cc_final: 0.7984 (tp) REVERT: C 175 GLN cc_start: 0.7312 (tt0) cc_final: 0.6721 (mp10) REVERT: C 186 LYS cc_start: 0.7665 (mptt) cc_final: 0.7335 (ttmm) outliers start: 7 outliers final: 3 residues processed: 75 average time/residue: 1.3988 time to fit residues: 110.1360 Evaluate side-chains 76 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7086 Z= 0.214 Angle : 0.532 5.525 9705 Z= 0.248 Chirality : 0.039 0.183 1056 Planarity : 0.005 0.047 1035 Dihedral : 12.931 121.583 2445 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.14 % Allowed : 11.27 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.31), residues: 714 helix: 2.19 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.07 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 190 HIS 0.002 0.001 HIS C 125 PHE 0.023 0.001 PHE A 144 TYR 0.013 0.001 TYR B 177 ARG 0.002 0.000 ARG C 244 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6852 (ttt90) REVERT: A 183 LYS cc_start: 0.8265 (ttpp) cc_final: 0.8037 (ttpp) REVERT: A 186 LYS cc_start: 0.7754 (mptt) cc_final: 0.7440 (ttmm) REVERT: B 144 PHE cc_start: 0.7645 (t80) cc_final: 0.7241 (t80) REVERT: B 186 LYS cc_start: 0.7797 (mptt) cc_final: 0.7485 (ttmm) REVERT: C 21 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.6635 (t0) REVERT: C 170 LEU cc_start: 0.8298 (tp) cc_final: 0.7986 (tp) REVERT: C 175 GLN cc_start: 0.7310 (tt0) cc_final: 0.6749 (mp10) REVERT: C 178 GLN cc_start: 0.8102 (mt0) cc_final: 0.7652 (mp10) REVERT: C 186 LYS cc_start: 0.7636 (mptt) cc_final: 0.7289 (ttmm) outliers start: 7 outliers final: 3 residues processed: 77 average time/residue: 1.4170 time to fit residues: 114.4595 Evaluate side-chains 79 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.5980 chunk 38 optimal weight: 0.0770 chunk 28 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.0870 chunk 64 optimal weight: 0.0030 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 overall best weight: 0.2726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7086 Z= 0.144 Angle : 0.483 5.580 9705 Z= 0.225 Chirality : 0.037 0.196 1056 Planarity : 0.005 0.049 1035 Dihedral : 12.314 106.585 2445 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.98 % Allowed : 11.60 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.32), residues: 714 helix: 2.41 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.97 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 161 HIS 0.002 0.000 HIS C 225 PHE 0.016 0.001 PHE A 144 TYR 0.007 0.001 TYR A 62 ARG 0.001 0.000 ARG C 244 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.612 Fit side-chains REVERT: A 21 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6583 (t0) REVERT: A 106 TYR cc_start: 0.8762 (m-10) cc_final: 0.8516 (m-80) REVERT: A 144 PHE cc_start: 0.7468 (t80) cc_final: 0.6700 (t80) REVERT: A 183 LYS cc_start: 0.8311 (ttpp) cc_final: 0.8092 (ttpp) REVERT: B 21 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6647 (t0) REVERT: B 24 LEU cc_start: 0.7901 (tp) cc_final: 0.7636 (tp) REVERT: B 144 PHE cc_start: 0.7600 (t80) cc_final: 0.7263 (t80) REVERT: B 186 LYS cc_start: 0.7784 (mptt) cc_final: 0.7497 (ttmm) REVERT: C 21 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.6689 (t0) REVERT: C 178 GLN cc_start: 0.7965 (mt0) cc_final: 0.7469 (mp10) outliers start: 6 outliers final: 1 residues processed: 97 average time/residue: 1.1581 time to fit residues: 118.7211 Evaluate side-chains 84 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain C residue 21 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 66 optimal weight: 0.0870 chunk 57 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7086 Z= 0.189 Angle : 0.528 6.425 9705 Z= 0.247 Chirality : 0.038 0.198 1056 Planarity : 0.005 0.046 1035 Dihedral : 12.299 104.140 2445 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.98 % Allowed : 12.42 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.31), residues: 714 helix: 2.29 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.85 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.002 0.000 HIS B 225 PHE 0.020 0.001 PHE A 144 TYR 0.009 0.001 TYR C 62 ARG 0.003 0.000 ARG B 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.697 Fit side-chains REVERT: A 21 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.6758 (t0) REVERT: A 106 TYR cc_start: 0.8764 (m-10) cc_final: 0.8512 (m-80) REVERT: B 21 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6684 (t0) REVERT: B 144 PHE cc_start: 0.7525 (t80) cc_final: 0.7132 (t80) REVERT: B 186 LYS cc_start: 0.7861 (mptt) cc_final: 0.7543 (ttmm) REVERT: C 21 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.6775 (t0) REVERT: C 178 GLN cc_start: 0.8022 (mt0) cc_final: 0.7601 (mp10) outliers start: 6 outliers final: 1 residues processed: 86 average time/residue: 1.2648 time to fit residues: 114.5816 Evaluate side-chains 85 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain C residue 21 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.126856 restraints weight = 6912.558| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.41 r_work: 0.3249 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7086 Z= 0.226 Angle : 0.553 5.918 9705 Z= 0.258 Chirality : 0.040 0.205 1056 Planarity : 0.005 0.046 1035 Dihedral : 12.291 102.504 2445 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.31 % Allowed : 12.25 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.31), residues: 714 helix: 2.21 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.96 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 161 HIS 0.002 0.001 HIS C 125 PHE 0.026 0.001 PHE A 144 TYR 0.011 0.001 TYR B 154 ARG 0.002 0.000 ARG A 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2431.19 seconds wall clock time: 44 minutes 25.72 seconds (2665.72 seconds total)